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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

9YDB

Eukaryotic pre-60S ribosomes from uL16 P-site loop mutants in bypass condition. Lsg1,Nmd3 and Tif6 present

This is a non-PDB format compatible entry.
Functional Information from PROSITE/UniProt
site_idPS00028
Number of Residues23
DetailsZINC_FINGER_C2H2_1 Zinc finger C2H2 type domain signature. Cnc..CviqFktsdlqryHmktewH
ChainResidueDetails
zCYS8-HIS30
site_idPS00049
Number of Residues27
DetailsRIBOSOMAL_L14 Ribosomal protein L14 signature. AIVVrqakswrrr.DGvflyFedNagVI
ChainResidueDetails
LXALA76-ILE102
site_idPS00050
Number of Residues16
DetailsRIBOSOMAL_L23 Ribosomal protein L23 signature. KKAYVRLTadydaldI
ChainResidueDetails
LZLYS120-ILE135
site_idPS00051
Number of Residues17
DetailsRIBOSOMAL_L39E Ribosomal protein L39e signature. RTnntIryNakrRNWRR
ChainResidueDetails
LnARG30-ARG46
site_idPS00299
Number of Residues26
DetailsUBIQUITIN_1 Ubiquitin domain signature. KskIqDkegIPpdqQrLIFaGkqleD
ChainResidueDetails
LoLYS27-ASP52
site_idPS00358
Number of Residues17
DetailsRIBOSOMAL_L5 Ribosomal protein L5 signature. LeqLSGQtpVqSkARyT
ChainResidueDetails
LMLEU37-THR53
site_idPS00430
Number of Residues68
DetailsTONB_DEPENDENT_REC_1 TonB-dependent receptor (TBDR) proteins signature 1. mtaqqapkwypsedvaapkktrkavrpqklraslvpgtvlillagrfrgkrvvylkhled.......................................................NTLLVTGP
ChainResidueDetails
LHMET1-PRO68
site_idPS00464
Number of Residues25
DetailsRIBOSOMAL_L22 Ribosomal protein L22 signature. RrrTyRAhGRinkyesspSHIELvV
ChainResidueDetails
LRARG126-VAL150
site_idPS00467
Number of Residues12
DetailsRIBOSOMAL_L2 Ribosomal protein L2 signature. PktRGVAmNPvD
ChainResidueDetails
LDPRO197-ASP208
site_idPS00474
Number of Residues24
DetailsRIBOSOMAL_L3 Ribosomal protein L3 signature. FeqnemiDaiAvTkGHGfeGvthR
ChainResidueDetails
LEPHE209-ARG232
site_idPS00475
Number of Residues32
DetailsRIBOSOMAL_L15 Ribosomal protein L15 signature. KILGkGrIpnvp.ViVkarfVSklAeekIraaG
ChainResidueDetails
LcLYS111-GLY142
site_idPS00526
Number of Residues20
DetailsRIBOSOMAL_L19E Ribosomal protein L19e signature. QKRLaAsvvgVGkrkVWLDP
ChainResidueDetails
LTGLN7-PRO26
site_idPS00579
Number of Residues15
DetailsRIBOSOMAL_L29 Ribosomal protein L29 signature. SLPKIKtVRKSIACV
ChainResidueDetails
LjSER40-VAL54
site_idPS00580
Number of Residues21
DetailsRIBOSOMAL_L32E Ribosomal protein L32e signature. FkRhhsdRyhRVaen..WRKqkG
ChainResidueDetails
LgPHE17-GLY37
site_idPS00634
Number of Residues33
DetailsRIBOSOMAL_L30 Ribosomal protein L30 signature. VLqlLrLtRinSgTfvkvtkatleLLklIepYV
ChainResidueDetails
LIVAL102-VAL134
site_idPS00700
Number of Residues22
DetailsRIBOSOMAL_L6_2 Ribosomal protein L6 signature 2. QicrVrnKdiRkFlDGIYVshK
ChainResidueDetails
LKGLN163-LYS184
site_idPS00709
Number of Residues25
DetailsRIBOSOMAL_L30E_1 Ribosomal protein L30e signature 1. SgkytlGyKstVKslRqGksKlIII
ChainResidueDetails
LeSER20-ILE44
site_idPS00783
Number of Residues24
DetailsRIBOSOMAL_L13 Ribosomal protein L13 signature. LRGMVShktarGKaalerLkVFeG
ChainResidueDetails
LQLEU84-GLY107
site_idPS00939
Number of Residues27
DetailsRIBOSOMAL_L1E Ribosomal protein L1e signature. NhneKryATaSAIaATAvaslvlaRGH
ChainResidueDetails
LFASN114-HIS140
site_idPS00993
Number of Residues21
DetailsRIBOSOMAL_L30E_2 Ribosomal protein L30e signature 2. ELGTavGKlfrvgvVsIlEaG
ChainResidueDetails
LeGLU76-GLY96
site_idPS01073
Number of Residues18
DetailsRIBOSOMAL_L24E Ribosomal protein L24e signature. FsGakIyPGrGtlFvRgD
ChainResidueDetails
LYPHE8-ASP25
site_idPS01077
Number of Residues20
DetailsRIBOSOMAL_L37E Ribosomal protein L37e signature. GTpSfGkRhnks.HtlCnRCG
ChainResidueDetails
LlGLY4-GLY23
site_idPS01082
Number of Residues18
DetailsRIBOSOMAL_L7AE Ribosomal protein L7Ae signature. CkkmgVPYaiVkGKarLG
ChainResidueDetails
LJCYS170-GLY187
site_idPS01104
Number of Residues15
DetailsRIBOSOMAL_L13E Ribosomal protein L13e signature. RaGRGFTLaEVkaaG
ChainResidueDetails
LNARG70-GLY84
site_idPS01105
Number of Residues22
DetailsRIBOSOMAL_L35AE Ribosomal protein L35Ae signature. GKVtRtHGnsGvVrAtFrnnLP
ChainResidueDetails
LhGLY69-PRO90
site_idPS01106
Number of Residues18
DetailsRIBOSOMAL_L18E Ribosomal protein L18e signature. KaLflSKinRPpVSVsRI
ChainResidueDetails
LSLYS50-ILE67
site_idPS01107
Number of Residues12
DetailsRIBOSOMAL_L27E Ribosomal protein L27e signature. GKNqWFFskLRF
ChainResidueDetails
LbGLY125-PHE136
site_idPS01108
Number of Residues18
DetailsRIBOSOMAL_L24 Ribosomal protein L24 signature. DDeVlVVrGskKGqe.GkI
ChainResidueDetails
LaASP53-ILE70
site_idPS01144
Number of Residues15
DetailsRIBOSOMAL_L31E Ribosomal protein L31e signature. VRLApeLNqAiWkRG
ChainResidueDetails
LfVAL49-GLY63
site_idPS01145
Number of Residues14
DetailsRIBOSOMAL_L34E Ribosomal protein L34e signature. TrSnKikvvKTPGG
ChainResidueDetails
LiTHR15-GLY28
site_idPS01170
Number of Residues19
DetailsRIBOSOMAL_L6E Ribosomal protein L6e signature. NgvPLRRvnarYVIATSt.K
ChainResidueDetails
LHASN72-LYS90
site_idPS01171
Number of Residues26
DetailsRIBOSOMAL_L21E Ribosomal protein L21e signature. GDiVdikangsiqk.GmpHkfYqGkTG
ChainResidueDetails
LVGLY37-GLY62
site_idPS01172
Number of Residues12
DetailsRIBOSOMAL_L44E Ribosomal protein L44e signature. KtTKKvvLRleC
ChainResidueDetails
LqLYS63-CYS74
site_idPS01190
Number of Residues11
DetailsRIBOSOMAL_L36E Ribosomal protein L36e signature. PYERRlIDLIR
ChainResidueDetails
LkPRO52-ARG62
site_idPS01194
Number of Residues24
DetailsRIBOSOMAL_L15E Ribosomal protein L15e signature. DKARrLGYkAkqGFVIYRvRVrRG
ChainResidueDetails
LPASP46-GLY69
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues8
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17287358","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues9
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"19779198","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues40
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"22106047","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues1
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"17330950","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues1
DetailsModified residue: {"description":"Pros-methylhistidine","evidences":[{"source":"PubMed","id":"20864530","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24865971","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"26826131","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues85
DetailsRegion: {"description":"C-terminal-extended nuclear localization signal","evidences":[{"source":"PubMed","id":"25936803","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues1
DetailsModified residue: {"description":"N-acetylserine","evidences":[{"source":"PubMed","id":"1544921","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues1
DetailsModified residue: {"description":"Omega-N-methylarginine","evidences":[{"source":"PubMed","id":"26046779","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17330950","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"19779198","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues1
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"Q02326","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues14
DetailsRepeat: {"description":"1"}
ChainResidueDetails
site_idSWS_FT_FI12
Number of Residues16
DetailsRepeat: {"description":"2"}
ChainResidueDetails
site_idSWS_FT_FI13
Number of Residues49
DetailsRegion: {"description":"2 X 15-17 AA approximate repeats"}
ChainResidueDetails
site_idSWS_FT_FI14
Number of Residues1
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17330950","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI15
Number of Residues2
DetailsModified residue: {"description":"N6,N6,N6-trimethyllysine","evidences":[{"source":"PubMed","id":"22522802","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI16
Number of Residues2
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"P40212","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI17
Number of Residues48
DetailsRegion: {"description":"Disordered","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}
ChainResidueDetails
site_idSWS_FT_FI18
Number of Residues47
DetailsCompositional bias: {"description":"Basic residues","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}
ChainResidueDetails
site_idSWS_FT_FI19
Number of Residues1
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"17287358","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI20
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"UniProtKB","id":"Q12672","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI21
Number of Residues1
DetailsModified residue: {"description":"N-acetylserine","evidences":[{"source":"PubMed","id":"16096273","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22814378","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI22
Number of Residues2
DetailsModified residue: {"description":"N6,N6-dimethyllysine; by RKM1","evidences":[{"source":"PubMed","id":"17327221","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI23
Number of Residues1
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P24000","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI24
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)","evidences":[{"source":"PubMed","id":"15542864","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI25
Number of Residues12
DetailsMotif: {"description":"Nuclear localization signal","evidences":[{"source":"PubMed","id":"2104804","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI26
Number of Residues1
DetailsModified residue: {"description":"N-acetylalanine; partial","evidences":[{"source":"PubMed","id":"10601260","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI27
Number of Residues1
DetailsModified residue: {"description":"N-acetylthreonine","evidences":[{"source":"PubMed","id":"10601260","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI28
Number of Residues18
DetailsZinc finger: {"description":"C4-type","evidences":[{"evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI29
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"22096102","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI30
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PDB","id":"4V8T","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI31
Number of Residues1
DetailsModified residue: {"description":"N6-methyllysine; by RKM3","evidences":[{"source":"PubMed","id":"18957409","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22522802","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24517342","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI32
Number of Residues1
DetailsModified residue: {"description":"N6-methyllysine; by RKM4","evidences":[{"source":"PubMed","id":"18957409","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24517342","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI33
Number of Residues21
DetailsZinc finger: {"description":"C4-type"}
ChainResidueDetails
site_idSWS_FT_FI34
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine; by CK1","evidences":[{"source":"HAMAP-Rule","id":"MF_03132","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI35
Number of Residues6
DetailsBinding site: {"evidences":[{"evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI36
Number of Residues7
DetailsBinding site: {"evidences":[{"evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

260320

PDB entries from 2026-09-30

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